The transcriptome of primary colorectal cancer: In order to characterize patterns of global transcriptional deregulation in primary colon carcinomas, we performed gene expression profiling of 73 tumors (UICC stage II, n=33 and UICC stage III, n=40) using oligonucleotide microarrays. For 30 of the tumors, expression profiles were compared to those from matched normal mucosa samples. We identified a set of 1,950 genes with highly significant deregulation between tumors and mucosa samples (P<1e-7). A significant proportion of these genes mapped to chromosome 20 (P=0.01). Seventeen genes had a greater than five-fold average expression difference between normal colon mucosa and carcinomas, including up-regulation of MYC and of HMGA1, a putative oncogene. Furthermore, we identified 68 genes that were significantly differentially expressed between lymph node negative and positive tumors (P<0.001), the functional annotation of which revealed a preponderance of genes that play a role in cellular immune response and surveillance. Taken together, our results demonstrate that both the high-level, significant transcriptional deregulation of specific genes and general modification of the average transcriptional activity of genes residing on aneuploid chromosomes coexist in rectal adenocarcinomas. The systematic comparison of colon and rectal carcinomas revealed a significant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/b-catenin signaling cascade, suggesting similar pathogenic pathways. Systematic knockdown of candidate colorectal cancer genes using RNA interference: The comprehensive and systematic analyses of gene expression profiles in primary colorectal carcinomas have suggested the involvement of several key regulators of malignant transformation of colorectal epithelium. We are now engaged in exploring the effects of these specific transcriptional changes on the transcriptome of colorectal cancer cells. In order to do so we have carefully generated a list of most significantly deregulated genes, validated their aberrant expression pattern in established cell lines from colorectal carcinomas, and designed siRNA oligonucleotides against them. We are now conducting systematic screens to explore the relative contribution of knockdown of all these genes on colon cancer viability. The effects of knockdown are measured both with cellular assays, such as assays for apoptosis and proliferation, as well as through measurement of the expression changes of a set of signature genes in colon cancer (using the QuantiGene Plex platform). This will pinpoint possible signaling pathways affected by these novel genes. Chromosomal breakpoints in primary colon cancer cluster at sites of structural variants in the genome: Genomic aberrations on chromosome 8 are common in colon cancer and are associated with lymph node and distant metastases, and with disease susceptibility. This prompted us to generate a high-resolution map of genomic imbalances of chromosome 8 in 51 primary carcinomas using a custom-designed genomic array consisting of a tiling path of BAC clones. Strikingly, we observed a significant association of chromosomal breakpoints with structural variants in the human genome: 41 per cent of all copy number changes occurred at sites of such copy number variants (p<2.2e-16). Such an association has not been described before and reveals a yet underappreciated plasticity of the colon cancer genome; it also points to potential mechanisms for the induction of chromosomal breakage in cancer cells. Response prediction of rectal adenocarcinomas to preoperative chemoradiotherapy: There is a wide spectrum of tumor responsiveness of rectal adenocarcinomas to preoperative chemoradiotherapy ranging from complete response to complete resistance. We were therefore interested to investigate whether parallel gene expression profiling of the primary tumor can contribute to stratification of patients into groups of responders or non-responders. Our results suggest that pre-therapeutic gene expression profiling may assist in response prediction of rectal adenocarcinomas to preoperative chemoradiotherapy. The implementation of gene expression profiles for treatment stratification and clinical management of cancer patients requires validation in large, independent studies, which are now under way